title: Functional characterization of liver enhancers that regulate drug-associated transporters.
abstract: Little is known about how genetic variations in enhancers influence drug response. In this study, we investigated whether nucleotide variations in enhancers that regulate drug transporters can alter their expression levels. Using comparative genomics and liver-specific transcription factor binding site (TFBS) analyses, we identified evolutionary conserved regions (ECRs) surrounding nine liver membrane transporters that interact with commonly used pharmaceuticals. The top 50 ECRs were screened for enhancer activity in vivo, of which five--located around ABCB11, SLC10A1, SLCO1B1, SLCO1A2, and SLC47A1--exhibited significant enhancer activity. Common variants identified in a large ethnically diverse cohort (n = 272) were assayed for differential enhancer activity, and three variants were found to have significant effects on reporter activity as compared with the reference allele. In addition, one variant was associated with reduced SLCO1A2 mRNA expression levels in human liver tissues, and another was associated with increased methotrexate (MTX) clearance in patients. This work provides a general model for the rapid characterization of liver enhancers and identifies associations between enhancer variants and drug response.
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.
authors.forename: M J
authors.initials: MJ
authors.lastname: Kim
authors.forename: P
authors.initials: P
authors.lastname: Skewes-Cox
authors.forename: H
authors.initials: H
authors.lastname: Fukushima
authors.forename: S
authors.initials: S
authors.lastname: Hesselson
authors.forename: S W
authors.initials: SW
authors.lastname: Yee
authors.forename: L B
authors.initials: LB
authors.lastname: Ramsey
authors.forename: L
authors.initials: L
authors.lastname: Nguyen
authors.forename: J L
authors.initials: JL
authors.lastname: Eshragh
authors.forename: R A
authors.initials: RA
authors.lastname: Castro
authors.forename: C C
authors.initials: CC
authors.lastname: Wen
authors.forename: D
authors.initials: D
authors.lastname: Stryke
authors.forename: S J
authors.initials: SJ
authors.lastname: Johns
authors.forename: T E
authors.initials: TE
authors.lastname: Ferrin
authors.forename: P-Y
authors.initials: PY
authors.lastname: Kwok
authors.forename: M V
authors.initials: MV
authors.lastname: Relling
authors.forename: K M
authors.initials: KM
authors.lastname: Giacomini
authors.forename: D L
authors.initials: DL
authors.lastname: Kroetz
authors.forename: N
authors.initials: N
authors.lastname: Ahituv
mesh_terms: D000074020:ATP Binding Cassette Transporter, Subfamily B, Member 11; D018528:ATP-Binding Cassette Transporters / Q000235:genetics / Q000378:metabolism*; D000483:Alleles; D000818:Animals; D001665:Binding Sites; D001692:Biological Transport; D017124:Conserved Sequence; D005260:Female; D005786:Gene Expression Regulation; D014644:Genetic Variation; D023281:Genomics / Q000379:methods; D006801:Humans; D008099:Liver / Q000378:metabolism; D008297:Male; D008727:Methotrexate / Q000493:pharmacokinetics*; D051379:Mice; D027361:Organic Anion Transporters / Q000235:genetics / Q000378:metabolism*; D027701:Organic Cation Transport Proteins / Q000235:genetics / Q000378:metabolism*; D004364:Pharmaceutical Preparations / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D012333:RNA, Messenger / Q000378:metabolism; D044469:Racial Groups / Q000235:genetics; D014157:Transcription Factors
chemical_list: C093491:ABCB11 protein, human; D000074020:ATP Binding Cassette Transporter, Subfamily B, Member 11; D018528:ATP-Binding Cassette Transporters; D027361:Organic Anion Transporters; D027701:Organic Cation Transport Proteins; D004364:Pharmaceutical Preparations; D012333:RNA, Messenger; D014157:Transcription Factors; D008727:Methotrexate